Nonnegative systems play an important role in various fields such as (bio)chemistry, economy, population dynamics or even in transportation modeling where the state variables of the models are often physically constrained to be nonnegative. The aim of this book is to summarize and present computation based analysis results for certain classes of nonnegative models that are primarily applied in the description of biochemical processes, and are given in the form of nonlinear ordinary differential equations. Majority of the developed analysis methods are put into an optimization framework, and they include the stability analysis and control of quasi-polynomial systems, and the computation of preferred reaction network structures from kinetic system models.